Adolf Meyer-Abich spent his career as one of the most vigorous and varied advocates in the biological sciences. Primarily a philosophical proponent of holistic thought in biology, he also sought through collaboration with empirically oriented colleagues in biology, medicine, and even physics to develop arguments against mechanistic and reductionistic positions in the life sciences, and to integrate them into a newly disciplinary theoretical biology. He participated in major publishing efforts including the founding of Acta Biotheoretica. He also sought international contacts (...) and worked for long stretches in Chile, the Dominican Republic, El Salvador, and the United States. His career straddled the Nazi period, which led him into a complex dance of support for and resistance to the regime. Despite the relative failure of his conceptual innovations to catch on, his ideas and writings sit squarely within the trajectory of thought and argument that has led to today’s reinvigoration of thought about conceptual integration in evolutionary developmental biology. (shrink)

We argue that the transition from unicellular to multicellular systems raises important conceptual challenges for understanding agency. We compare several MC systems displaying different forms of collective behavior, and we analyze whether these actions can be considered organismically integrated and attributable to the whole. We distinguish between a ‘constitutive’ and an ‘interactive’ dimension of organizational complexity, and we argue that MC agency requires a radical entanglement between the related processes which we call “the constitutive-interactive closure principle”. We explain in detail (...) that this is not possible without a regulatory center functionally integrating the two dimensions, and we also argue that, in turn, this type of regulation would not be possible without a special type of organization between the cells required for the development and maintenance of systems capable of integrated behavior. (shrink)

In this paper, I argue that starting with the organelles that constitute a cell – and continuing up the hierarchy of components in processes and subsystems of an organism – there are clear instances of emergent biological phenomena that can be considered “living” entities. These components and their attending processes are living emergent phenomena because of the way in which the components are organized to maintain homeostasis of the organism at the various levels in the hierarchy. I call this view (...) the homeostatic organization view of biological phenomena and, as is shown, it comports well with the standard philosophical accounts of nomological emergence and representational emergence. To proffer HOV, I describe properties of biological entities that include internal-hierarchical data exchange, data selectivity, informational integration, and environmental-organismic information exchange. Further, a distinction is drawn between particularized homeostasis and generalized homeostasis, and I argue that because the various processes and subsystems of an organism are functioning properly in their internal environments , the organism is able to exist as a hierarchically-organized entity in some environment external to it . Stated simply: that components of biological phenomena are organized to perform some function resulting in homeostasis marks them out to be living emergent entities distinguishable, in description and in reality, from the very physico-chemical processes of which they are composed. (shrink)

PDF version This talk explores three concepts of system in engineering: systems theory, systems approach, and systems engineering. They are exemplified in three dimensions of engineering: science, design, and management. Unifying the three system concepts is the idea of function: functional abstraction in theory, functional analysis in design, and functional requirements in management. Signifying what a system is for, function is a purposive notion absent in physical science, which aims to understand nature. It is prominent in engineering, which aims to (...) transform nature for serving the wants and needs of people. (shrink)

Adaptations during phylogenesis or ontogenesis can occur either by maintaning constant or by increasing the informational content of the organism. In the former case the increasing adaptations to external perturbation are achieved by increasing the rate of genome replication; the increased amount of DNA reflects an increase of total but not of law informational content. In the latter case the adaptations are achieved by either istructionist or evolutionary mechanism or a combination of both. Evolutionary adaptations occur during ontogenesis mainly in (...) the brain-mind, immunological and receptor systems and involve a repertoire of receptors that are., clonally distributed, genome-conditioned and amplified by somatic mutation. Specificity and intensity of responses are achieved a posteriori as a result of natural selection of the clones. The major adaptations during phylogenesis are accompanied by increased complexity. They have been attributed to shifts, short in time and space, against the entropic drive and thus occur notwithstanding the entropic drive and the second law of thermodynamics. The alternative view, is that the generation of complexity is due to the second law of thermodynamics in its extended formulation which includes Prigogine's theorem of minimum entropy production. This view requires however that natural selection provides the biological system with structures that bring the reactions within Onsager's range. The hierarchical organization of the natural world thus reflects a stratified thermodynamic stability. As the evolutionary adaptations generate new information they may be assimilated to Marxwell demon type of processes. (shrink)

Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for treating diseases such as cancers, is (...) pointed out. The roles played by multiple metastable states in the “continuous uphill flow of Life” supported through internal bioenergetic processes that are coupled to essential inflows are also discussed in relation to dynamic realizations of (M,R)-systems. Furthermore, the roles played by the underlying, many-valued, quantum logics and symbolic computations for ultra-complex biological systems are also briefly discussed. (shrink)

Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction–Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA–Notch interaction can possibly have substantial impacts on neurite outgrowth and (...) on the process of axon formation. This can be observed by the numerical study of the homogeneous system showing that in the absence of RA–Notch interaction the unperturbed homogeneous system may exhibit different saddle-node bifurcations that are robust under small perturbations by low levels of RA–Notch interactions, while large increases in the level of RA–Notch interaction result in a number of transitions of saddle-node bifurcations into Hopf bifurcations. It is speculated that near a Hopf bifurcation, the regulations between the positive and negative feedbacks change in such a way that spontaneous symmetry breaking takes place only when transport of activated Notch protein takes place at a faster rate. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

The levels that compose biological hierarchies each have their own energetic, spatial and temporal structure. Indeed, it is the discontinuity in energy relationships between levels, as well as the similarity of sub-systems that support them, that permits levels to be defined. In this paper, the temporal structure of living hierarchies, in particular that pertaining to Human society, is examined. Consideration is given to the period defining the lifespan of entities at each level and to a periodic event considered fundamental to (...) the maintenance of that level. The ratio between the duration of these two periods is found to be approximately 2.5 × 104. A similar relationship is found when lower, non-living levels of molecules and atoms are considered. This suggests that there is a constant factor of amplification between analogous periodic events at successive levels of the Human hierarchy. (shrink)

Using the Burgess Shale controversies as a case-study, this paper argues that controversies within different domains may interact as to create a situation of "complicated intricacies," where the practicing scientist has to navigate through a context of multiple thought collectives. To some extent each of these collectives has its own dynamic complete with fairly negotiated standards for investigation and explanation, theoretical background assumptions and certain peculiarities of practice. But the intellectual development in one of these collectives may "spill over" having (...) far reaching consequences for the treatment of apparently independent epistemic problems that are subject of investigation in other thought collectives. For the practicing scientist it is necessary to take this complex web of interactions into account in order to be able to navigate in such a situation. So far most studies of academic science have had a tendency to treat the practicing scientist as members of a single (enclosed) thought collective that stands intellectually isolated from other similar entities unless the discipline was in a state of crisis of paradigmatic proportions. The richness and complexity of Burgess Shale debate shows that this encapsulated kind of analysis is not enough. (shrink)

Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting.

This thematic issue addresses questions of constraints on the evolution of form—physical, biological, and technical. Here, form is defined as an embodiment of a specific structure, which can be hierarchically different yet emerge from the same processes. The focus of this contribution is about how developmental biology and paleontology can be better integrated and compared in order to produce hypotheses about the evolution of form. The constraints on current EvoDevo research stem from the disconnect in the focus of study for (...) developmental geneticists and evolutionary morphologists; the former being interested in early developmental events at a molecular level in a model animal, the latter in late developmental events or comparison between adult forms, at a structural level in non-model animals. In order to truly integrate information from both fields in our understanding of evolutionary processes, morphology needs to be reintegrated in the study of gene expression, and its time frame needs to be extended beyond early developmental stages. Gene expression in non-model organisms also needs to be studied in order to gain perspective into primitive patterning at evolutionary nodes. Hypotheses formed by the comparison of expression patterns and morphologies seen in extant species can then be tested against forms found in the fossil record, coming closer to understanding the mechanisms underlying evolution. (shrink)

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...) equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena, where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations. I offer general conclusions for philosophical accounts of explanation. (shrink)

"By combining recent advances in the physical sciences with some of the novel ideas, techniques, and data of modern biology, this book attempts to achieve a new and different kind of evolutionary synthesis. I found it to be challenging, fascinating, infuriating, and provocative, but certainly not dull."--James H, Brown, University of New Mexico "This book is unquestionably mandatory reading not only for every living biologist but for generations of biologists to come."--Jack P. Hailman, Animal Behaviour , review of the first (...) edition "An important contribution to modern evolutionary thinking. It fortifies the place of Evolutionary Theory among the other well-established natural laws."--R.Gessink, TAXON. (shrink)

Recent work on epistemic integration in the life sciences has emphasized the importance of integration in thinking about explanatory practice in science, particularly for articulating a robust alternative to reductionism and anti-reductionism. This paper analyzes the role of models in balancing the relative contributions of lower- and higher-level epistemic resources involved in this process. Integration between multiple disciplines proceeds by constructing a problem agenda (Love 2008), a set of interrelated problems that structures the problem space of a complex phenomenon that (...) is investigated by many disciplines. The usage of models, it is argued, mark changes in a phenomenon’s problem agenda depending on the task that is expected of it. Particularly, it emphasizes the sensitivity of a problem agenda to changing attitudes in the solutions to the conceptual and empirical items constituting that agenda. The analysis will proceed by means of a case study, the Reichardt motion detector, a model that has been vital to the methodological and conceptual development of research on motion detection, especially in invertebrates. As will be seen, the history of the Reichardt model will exemplify the dynamic changes that occur in the interdisciplinary negotiations that comprise the active efforts of various sciences working to integrate their resources. (shrink)

The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

Biology deals, notoriously, with complex systems. In discussing biological methodology, all three papers in this symposium honor the complexity of biological subject matter by preferring models and theories built to reflect the details of complex systems to models based on broad general principles or laws. Rheinberger's paper, the most programmatic of the three, provides a framework for the epistemology of discovery in complex systems. A fundamental problem is raised for Rheinberger's epistemology, namely, how to understand the referential continuity of the (...) theoretical terms and concepts employed in typical case studies involving complex systems. (shrink)

In recent years a new conceptual tool called Complexity Theory has come to the attention of scientists and philosophers. This approach is concerned with the emergent properties of interacting systems. It has found wide applicability from cosmology to Social Structure Analysis. However, practitioners are still struggling to find the best way to define complexity and then to measure it. A new book Complexity and the arrow of time by Lineweaver et al. contains contributions from scholars who provide critical reviews of (...) Complexity Theory and its wider applications. This is a huge task and this essay examines how well the authors have succeeded in satisfying the claim made by the book’s three editors to have clarified the leading questions. I also explore the application of Complexity Theory to Biology as a means to explain the popular view that biological complexity has increased over time. In this regard, I conclude by recommending an Information Theory approach which urges that physical complexity arises from accumulation of genetic coding sequences. (shrink)

The present thesis, compatible with Darwinian theory, endeavours to provide original answers to the question of why the evolution of species leads to beings more complex than those existing before. It is based on the repetition of two main principles alleged to play a role in evolution towards complexity, i.e. "juxtaposition" and "integration". Juxtaposition is the addition of identical entities. Integration is the modification, or specialisation, of these entities, leading to entities on a higher level, which use the previous entities (...) as units. Several concrete examples of the process are given, at the genetic level (introns), at the anatomical level and at the social level. Structures where integration at one level leaves the units at a lower level in a state of relative autonomy can be describedusing the metaphor of the "mosaic", and the description can also be applied to the human brain and functioning of thought, where essential functions such as language or memory have a mosaic structure. (shrink)

A fundamental misapprehension of the nature of our being in the world underlies the general inhumanity and incoherence of modern culture. The belief that abstraction as a mode of knowing can be universalized to provide a rational ground for all human knowledge and action is a pernicious and unacknowledged background to several modern diseases. Illustrative of these maladies is the seeming dichotomy between the aesthetic and the analytic approaches to nature. One critical arena in which the incoherences of our current (...) understandings of our place in nature come to light is in the battle over the environment. I argue that a more adequate conceptualization of our place in the natural world can be erected if the central metaphors for our understanding are grounded in notions derived from the sciences of life. The key concepts must include contingency, historicity, evolution, organism, and imaginative interaction with concrete reality in individual human beings. (shrink)

Complexly organized systems include biological and cognitive systems, as well as many of the everyday systems that form our environment. They are both common and important, but are not well understood. A complex system is, roughly, one that cannot be fully understood via analytic methods alone. An organized system is one that shows spatio-temporal correlations that are not determined by purely local conditions, though organization can be more or less localizable within a system. Organization and complexity can vary independently to (...) some extent, but they are interconnected: organisation requires some complexity, but complexity cannot be maximum in an organized system. I will define complexity and organization more precisely, and show how these definitions imply the above properties. Next I will discuss how organized complexity can be modelled, with an eye to limitations on the tractability of both the models and the modelling process. I will finish with some remarks on the limits of our possible understanding of complexly organized systems. Keywords: complexity, organization, modelling, holism, information theory.. (shrink)

Scientists have attempted several times to define the notion of complexity. A proper definition uses elements of three sets: a set of sites, as set of connections, and a set of nodes coincides with the set. Sites and connections can be translated into terms of graph theory as vertices and edges, which enables to consider complexity as an associated graph.Thus complexity of a system (or a structure) will be defined as the number of possible figures and aspects which are obtained (...) by combining vertices and edges. Complexity is the product of two factors, the first factor is tied to the combination of nodes called mutability and the second is tied to the combination of edges called liability. (shrink)

Communication and recognition are essential for social life. Social insects are good model systems to study social behavior and complexity because their societies are evolutionarily stable and ecologically successful. Ants, in particular, show a large variety of adaptations and are extremely diverse. In ants, social interactions are regulated by at least three levels of recognition. Nestmate recognition occurs between colonies, is very effective, and involves fast processing. Within a colony, division of labor is enhanced by recognition of different classes of (...) individuals. Ultimately, in particular circumstances, such as cooperative colony founding with stable dominance hierarchies, ants are capable of individual recognition. The underlying recognition cues and mechanisms appear to be specific to each recognition level, and their integrated understanding could contribute to the identification of the minimum requirements for the emergence of sociality. (shrink)

Book review of Bechtel and Richardson, Discovering Complexity (1993). Review suggests that one theme of the book -- that scientific reason is "constituted" in part by a cognitive strategy of finding complexity -- is not fully supported.

There are two different ways of defining complexity.1) Traditionally, the word "complexity" is considered synonymous to "organization". The transformation of species is an expression of victory against random indifferencism.

Catastrophe Theory was developed in an attempt to provide a form of Mathematics particularly apt for applications in the biological sciences. It was claimed that while it could be applied in the more conventional physical way, it could also be applied in a new metaphysical way, derived from the Structuralism of Saussure in Linguistics and Lévi-Strauss in Anthropology.Since those early beginnings there have been many attempts to apply Catastrophe Theory to Biology, but these hopes cannot be said to have been (...) fully realised. (shrink)

Darwin's greatest accomplishment was to show how life might be explained as the result of natural selection. But does Darwin's theory mean that life was unintended? William A. Dembski argues that it does not. In this book Dembski extends his theory of intelligent design. Building on his earlier work in The Design Inference (Cambridge, 1998), he defends that life must be the product of intelligent design. Critics of Dembski's work have argued that evolutionary algorithms show that life can be explained (...) apart from intelligence. But by employing powerful recent results from the No Free Lunch Theory, Dembski addresses and decisively refutes such claims. As the leading proponent of intelligent design, Dembski reveals a designer capable of originating the complexity and specificity found throughout the cosmos. Scientists and theologians alike will find this book of interest as it brings the question of creation firmly into the realm of scientific debate. (shrink)

In The Evolution of biological complexity, Christoph Adami, Charles Ofria and Travis C. Collier analysed the relationship between evolution by natural selection and the entropy of the genome. There are some similarities between their paper and my own analysis of.